the aching is from 2 things, 1st of all when u exercise u build up lactic acid as a waste product in your muscles this can cause the aching ur now experiencing
to get rid of it make sure u stretch before and after ur workout, however stretch oly lightly before hand (this is relating to performance and output but dont worry about it too much just stretch light at the start and longer at the end)
also be sure to take it plenty of water, u need 2-4 litres a day anyway but when ur exercising u need to replace the fluid you are losing
the 2nd thing is as u exercise u are breaking down the connections with ur muscles fibres, essentially making loads of tiny little tears, when you stop and recover, mostly during sleep the muscle fibres rebond stronger than before, this is of course if you have enough protein to accomplish this
depending on your currently level of fitness and conditioning you may not be getting enough time to recover, be sure to rest, its very important
running is very low impact compared to say heavy lifting for example so you dont really need to be spending days on and off resting for ages to recover you probably arnt getting enough water, protein or sleep
make sure if u find ur legs aching you can do all of these to help;
massage them after excercise and while they are aching
get plenty of water before and after workouts
get plenty of protein
stretch light before exercise
stretch harder and longer after exercise
get enough rest, that means sleep!
